I think the issue may be that I can't seem to actually apply the settings to the duplicated file.
public static void main(String args) throws Exception
Workbook workbook = null;
workbook = Workbook.getWorkbook(new File("../someFile.xls"));
System.err.println(">>>>" + e.getMessage());
WritableWorkbook workbook2 = Workbook.createWorkbook(new File("output.xls"), workbook);
WritableSheet sheet = workbook2.getSheet(0);
SheetSettings setting = new SheetSettings(sheet);